Xyz poscar.pl: Difference between revisions

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New page: #!/usr/bin/perl -w ###############Edit this############### $title = "Single points"; $ncell = 25.832; ####################################### ###Parameters inicialization $i = $j = $k...
 
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#!/usr/bin/perl -w
go back to [[Main Page]], [[Computational Resources]], [[Scripts]], [[Scripts for VASP]]


###############Edit this###############
#!/usr/bin/perl -w
$title = "Single points";
$ncell =  25.832;


#######################################
###############Edit this###############
$title = "Single points";
$ncell =  25.832;


###Parameters inicialization
#######################################
$i = $j = $k = $l = $J = $m = 0;
 
$k = 1;
###Parameters inicialization
######
$i = $j = $k = $l = $J = $m = 0;
$k = 1;
######
        
        


###Enter the XYZ file   
###Enter the XYZ file   
chomp($arq_log = <STDIN>);
chomp($arq_log = <STDIN>);


#open file
#open file  
open(ARQ, "<$arq_log") or die "Check the file $arq_log: $!\n";
open(ARQ, "<$arq_log") or die "Check the file $arq_log: $!\n";
$arq_xyz = "$arq_log";
$arq_xyz = "$arq_log";


#replacing suffix: xyz=>vasp
#replacing suffix: xyz=>vasp
$arq_xyz =~ s/xyz/vasp/g;
$arq_xyz =~ s/xyz/vasp/g;


#regular expression, operations
#regular expression, operations
while (<ARQ>){
while (<ARQ>){
    if (/^\s(\w+)\s+(\-?\d+\.\d+)\s+(\-?\d+\.\d+)\s+(\-?\d+\.\d+)/){
    if (/^\s(\w+)\s+(\-?\d+\.\d+)\s+(\-?\d+\.\d+)\s+(\-?\d+\.\d+)/){
$atom[$i] = $1;
$atom[$i] = $1;
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$i++;
$i++;
    }
    }
}
}


#sorting the lines
#sorting the lines
@sorted_lines = sort @line;
@sorted_lines = sort @line;


#split sorted lines
#split sorted lines
foreach (@sorted_lines){
foreach (@sorted_lines){
                      if (/^(\w+)\s+(\-?\d+\.\d+)\s+(\-?\d+\.\d+)\s+(\-?\d+\.\d+)/){
                        if (/^(\w+)\s+(\-?\d+\.\d+)\s+(\-?\d+\.\d+)\s+(\-?\d+\.\d+)/){
  $Atom[$j] = $1;
          $Atom[$j] = $1;
  $X[$j] = $2;
          $X[$j] = $2;
  $Y[$j] = $3;
                $Y[$j] = $3;
  $Z[$j] = $4;
          $Z[$j] = $4;
                           #print "$j $Atom[$j] $X[$j], $Y[$j], $Z[$j]\n";
                           #print "$j $Atom[$j] $X[$j], $Y[$j], $Z[$j]\n";
  if ($j == 0){
  if ($j == 0){
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      #print "$l $k $Atom[$j] $natoms[$l]\n";
      #print "$l $k $Atom[$j] $natoms[$l]\n";
      $k++;
      $k++;
     
  }
  }
  else {
  else {
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$j++;  
$j++;  
      }
      }
}
}  




##################################
##################################
###Generation of the VASP file ###
###Generation of the VASP file ###
##################################
##################################


#open new file.vasp
#open new file.vasp
open(XYZ, ">$arq_xyz" ) or die "Check the file $arq_xyz : $!\n";
open(XYZ, ">$arq_xyz" ) or die "Check the file $arq_xyz : $!\n";


#######################
#######################
####Print preambulo####
####Print preambulo####
#######################
#######################


#Cell's data
#Cell's data
print XYZ " $title \n";
print XYZ " $title \n";
printf XYZ "  % 2.16f \n",$ncell;
printf XYZ "  % 2.16f \n",$ncell;
printf XYZ "    % 2.16f % 2.16f % 2.16f \n",1.0, 0.0, 0.0;
printf XYZ "    % 2.16f % 2.16f % 2.16f \n",1.0, 0.0, 0.0;
printf XYZ "    % 2.16f % 2.16f % 2.16f \n",0.0, 1.0, 0.0;
printf XYZ "    % 2.16f % 2.16f % 2.16f \n",0.0, 1.0, 0.0;
printf XYZ "    % 2.16f % 2.16f % 2.16f \n",0.0, 0.0, 1.0;
printf XYZ "    % 2.16f % 2.16f % 2.16f \n",0.0, 0.0, 1.0;




#Number of each atom's type N1 N2 N3 ....
#Number of each atom's type N1 N2 N3 ....
for($m = 1; $m <= $l; $m++){
for($m = 1; $m <= $l; $m++){
     print XYZ "  $natoms[$m]";
     print XYZ "  $natoms[$m]";
}
}
print XYZ "\n";
print XYZ "\n";
print XYZ "Selective dynamics\n";
print XYZ "Selective dynamics\n";
print XYZ "Direct\n";
print XYZ "Direct\n";
#######################
#######################




#print the cartesian to the new file.vasp
#print the cartesian to the new file.vasp
for($J = 0; $J < $i; $J++){
for($J = 0; $J < $i; $J++){


  printf XYZ " % 2.16f % 2.16f % 2.16f F  F  F \n",$X[$J], $Y[$J], $Z[$J];
  printf XYZ " % 2.16f % 2.16f % 2.16f F  F  F \n",$X[$J], $Y[$J], $Z[$J];


}  
}  
$J = 0;
$J = 0;


print XYZ "\n";  
print XYZ "\n";  


#Print the parameters to dinamics. (by now, only zeros)
#Print the parameters to dinamics. (by now, only zeros)
for($J = 0; $J < $i; $J++){
for($J = 0; $J < $i; $J++){


  printf XYZ " % 2.16f % 2.16f % 2.16f \n",0.0, 0.0, 0.0;
  printf XYZ " % 2.16f % 2.16f % 2.16f \n",0.0, 0.0, 0.0;
}


}
print XYZ "\n";
 
print XYZ "\n";


####Close the XYZ and VASP files
####Close the XYZ and VASP files


close(ARQ);
close(ARQ);
close(XYZ);
close(XYZ);

Latest revision as of 13:14, 13 September 2011

go back to Main Page, Computational Resources, Scripts, Scripts for VASP 

#!/usr/bin/perl -w

###############Edit this###############
$title = "Single points"; 
$ncell =  25.832;

#######################################

###Parameters inicialization
$i = $j = $k = $l = $J = $m = 0;
$k = 1;
######
     

###Enter the XYZ file  
chomp($arq_log = <STDIN>);

#open file 
open(ARQ, "<$arq_log") or die "Check the file $arq_log: $!\n";
$arq_xyz = "$arq_log";

#replacing suffix: xyz=>vasp
$arq_xyz =~ s/xyz/vasp/g;

#regular expression, operations
while (<ARQ>){

if (/^\s(\w+)\s+(\-?\d+\.\d+)\s+(\-?\d+\.\d+)\s+(\-?\d+\.\d+)/){ $atom[$i] = $1; $x[$i] = sprintf("%2.16f", $2/$ncell); $y[$i] = sprintf("%2.16f", $3/$ncell); $z[$i] = sprintf("%2.16f", $4/$ncell); 

               $line[$i] = "$atom[$i] $x[$i] $y[$i] $z[$i]";
         	#print "$line[$i]\n";

$i++; } 

}

#sorting the lines
@sorted_lines = sort @line;

#split sorted lines
foreach (@sorted_lines){
                        if (/^(\w+)\s+(\-?\d+\.\d+)\s+(\-?\d+\.\d+)\s+(\-?\d+\.\d+)/){

$Atom[$j] = $1; $X[$j] = $2; 

      		          $Y[$j] = $3;

$Z[$j] = $4; 

                         #print "$j $Atom[$j] $X[$j], $Y[$j], $Z[$j]\n";

if ($j == 0){ $l++; $natoms[$l] = $k; #print "$l $k $Atom[$j] $natoms[$l]\n"; $k++; } else { if ($Atom[$j -1] eq $Atom[$j] ){ $natoms[$l] = $k; #print "$l $k $Atom[$j] $natoms[$l]\n"; $k++; } else { $k=1; $l++; $natoms[$l] = $k; #print "$l $k $Atom[$j] $natoms[$l]\n"; $k++ } } $j++; } 

} 



##################################
###Generation of the VASP file ###
##################################

#open new file.vasp
open(XYZ, ">$arq_xyz" ) or die "Check the file $arq_xyz : $!\n";

#######################
####Print preambulo####
#######################

#Cell's data
print XYZ " $title \n";
printf XYZ "   % 2.16f \n",$ncell;
printf XYZ "     % 2.16f % 2.16f % 2.16f \n",1.0, 0.0, 0.0;
printf XYZ "     % 2.16f % 2.16f % 2.16f \n",0.0, 1.0, 0.0;
printf XYZ "     % 2.16f % 2.16f % 2.16f \n",0.0, 0.0, 1.0;



#Number of each atom's type N1 N2 N3 ....
for($m = 1; $m <= $l; $m++){
   print XYZ "  $natoms[$m]";
}
print XYZ "\n";
print XYZ "Selective dynamics\n";
print XYZ "Direct\n";
#######################



#print the cartesian to the new file.vasp
for($J = 0; $J < $i; $J++){

printf XYZ " % 2.16f % 2.16f % 2.16f F   F   F \n",$X[$J], $Y[$J], $Z[$J];

} 
$J = 0;

print XYZ "\n"; 

#Print the parameters to dinamics. (by now, only zeros)
for($J = 0; $J < $i; $J++){

printf XYZ " % 2.16f % 2.16f % 2.16f \n",0.0, 0.0, 0.0;

} 

print XYZ "\n";

####Close the XYZ and VASP files

close(ARQ);
close(XYZ);
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